85:, it applied to prediction of gene function. Before the use of phylogenomic techniques, predicting gene function was done primarily by comparing the gene sequence with the sequences of genes with known functions. When several genes with similar sequences but differing functions are involved, this method alone is ineffective in determining function. A specific example is presented in the paper "Gastronomic Delights: A movable feast". Gene predictions based on sequence similarity alone had been used to predict that
1349:
1026:
1361:
192:. Using this method, it is theoretically possible to create fully resolved phylogenetic trees, and timing constraints can be recovered more accurately. However, in practice this is not always the case. Due to insufficient data, multiple trees can sometimes be supported by the same data when analyzed using different methods.
113:
Traditional phylogenetic techniques have difficulty establishing differences between genes that are similar because of lateral gene transfer and those that are similar because the organisms shared an ancestor. By comparing large numbers of genes or entire genomes among many species, it is possible to
104:
was not in the same subfamily as those known to be involved in mismatch repair. Furthermore, he suggested that this "phylogenomic" approach could be used as a general method for prediction functions of genes. This approach was formally described in 1998. For reviews of this aspect of phylogenomics
38:
and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Four major areas fall under phylogenomics:
60:
The ultimate goal of phylogenomics is to reconstruct the evolutionary history of species through their genomes. This history is usually inferred from a series of genomes by using a genome evolution model and standard statistical inference methods (e.g.
95:. This prediction was based on the fact that this organism has a gene for which the sequence is highly similar to genes from other species in the "MutS" gene family which included many known to be involved in mismatch repair. However, Eisen noted that
134:. Often, such events are evolutionarily relevant. For example, multiple duplications of genes encoding degradative enzymes of certain families is a common adaptation in microbes to new nutrient sources. On the contrary, loss of genes is important in
99:
lacks other genes thought to be essential for this function (specifically, members of the MutL family). Eisen suggested a solution to this apparent discrepancy – phylogenetic trees of genes in the MutS family revealed that the gene found in
160:, and varying rates of evolution for different genes. By using entire genomes in these comparisons, the anomalies created from these factors are overwhelmed by the pattern of evolution indicated by the majority of the data. Through
151:
Traditional single-gene studies are effective in establishing phylogenetic trees among closely related organisms, but have drawbacks when comparing more distantly related organisms or microorganisms. This is because of
142:
events, which potentially duplicate all the genes in a genome at once, are drastic evolutionary events with great relevance in the evolution of many clades, and whose signal can be traced with phylogenomic methods.
214:
118:
of the organism. Using these methods, researchers were able to identify over 2,000 metabolic enzymes obtained by various eukaryotic parasites from lateral gene transfer.
164:, it has been discovered that most of the photosynthetic eukaryotes are linked and possibly share a single ancestor. Researchers compared 135 genes from 65 different
715:
Philippe H, Snell EA, Bapteste E, Lopez P, Holland PW, Casane D "Phylogenomics of eukaryotes: impact of missing data on large alignments
614:"The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes"
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126:
The comparison of complete gene sets for a group of organisms allows the identification of events in gene evolution such as
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730:
1119:
822:"Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny"
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1204:
1137:
1365:
1214:
1144:
361:
Simion P, Delsuc F, Phillipe H (2020). "2.1 To What Extent
Current Limits of Phylogenomics Can Be Overcome?".
66:
663:
Delsuc F, Brinkmann H, Philippe H (May 2005). "Phylogenomics and the reconstruction of the tree of life".
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identify transferred genes, since these sequences behave differently from what is expected given the
677:
473:"Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis"
920:
Philippe, Herve'; Delsuc, Frederic; Brinkmann, Henner; Lartillot, Nicolas (2005). "Phylogenomics".
139:
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Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, et al. (August 1997).
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data and evolutionary reconstructions. It is a group of techniques within the larger fields of
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Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K (February 2012).
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773:"Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes"
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see Brown D, Sjölander K. Functional classification using phylogenomic inference.
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dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PC, Yang Z (September 2012).
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573:"Phylogenomic inference of protein molecular function: advances and challenges"
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35:
30:. The term has been used in multiple ways to refer to analysis that involves
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432:"The complete genome sequence of the gastric pathogen Helicobacter pylori"
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318:(June 2008). "Evolution. Building the tree of life, genome by genome".
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Establishment and clarification of evolutionary relationships
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Jeffroy O, Brinkmann H, Delsuc F, Philippe H (April 2006).
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Burki F, Shalchian-Tabrizi K, Pawlowski J (August 2008).
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92:
611:
514:"Functional classification using phylogenomic inference"
662:
1021:
922:
Annual Review of
Ecology, Evolution, and Systematics
360:
16:
Intersection of the fields of evolution and genomics
138:, such as in intracellular parasites or symbionts.
871:"Phylogenomics of strongylocentrotid sea urchins"
1379:
380:
731:"Phylogenomics: the beginning of incongruence?"
612:Whitaker JW, McConkey GA, Westhead DR (2009).
511:
109:Prediction and retracing lateral gene transfer
72:
958:
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381:Eisen JA, Kaiser D, Myers RM (October 1997).
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168:of photosynthetic organisms. These included
147:Establishment of evolutionary relationships
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383:"Gastrogenomic delights: a movable feast"
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934:10.1146/annurev.ecolsys.35.112202.130205
255:BioMed Central | Fgenerated title -->
121:
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314:
268:"Statistics and truth in phylogenomics"
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22:is the intersection of the fields of
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371:
869:Kober KM, Bernardi G (April 2013).
423:
188:. This has been referred to as the
13:
512:Brown D, Sjölander K (June 2006).
14:
1404:
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1348:
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1200:Phylogenetic comparative methods
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826:Proceedings. Biological Sciences
364:Phylogenetics in the Genomic Era
1205:Phylogenetic niche conservatism
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272:Molecular Biology and Evolution
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590:10.1093/bioinformatics/bth021
332:10.1126/science.320.5884.1716
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67:maximum likelihood estimation
571:Sjölander K (January 2004).
539:10.1371/journal.pcbi.0020077
195:
7:
1125:Phylogenetic reconciliation
1032:Evolutionary biology portal
988:Computational phylogenetics
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73:Prediction of gene function
43:Prediction of gene function
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518:PLOS Computational Biology
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1315:Phylogenetic nomenclature
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750:10.1016/j.tig.2006.02.003
719:2004 Sep;21(9):1740-52. .
52:Prediction and retracing
875:BMC Evolutionary Biology
665:Nature Reviews. Genetics
631:10.1186/gb-2009-10-4-r36
367:. pp. 2.1.1–2.1.34.
218:(phylogenomics software)
140:Whole genome duplication
1195:Molecular phylogenetics
1145:Distance-matrix methods
993:Molecular phylogenetics
888:10.1186/1471-2148-13-88
471:Eisen JA (March 1998).
222:Microbial phylogenetics
190:Plants+HC+SAR megagroup
1215:Phylogenetics software
1129:Probabilistic methods
1078:Long branch attraction
838:10.1098/rspb.2012.0683
789:10.1098/rsbl.2008.0224
91:can repair mismatched
1008:Evolutionary taxonomy
284:10.1093/molbev/msr202
154:lateral gene transfer
122:Gene family evolution
54:lateral gene transfer
49:Gene family evolution
1167:Three-taxon analysis
1073:Phylogenetic network
1210:Phylogenetic signal
832:(1742): 3491–3500.
530:2006PLSCB...2...77B
399:10.1038/nm1097-1076
326:(5884): 1716–1717.
136:reductive evolution
88:Helicobacter pylori
1138:Bayesian inference
1133:Maximum likelihood
738:Trends in Genetics
490:10.1101/gr.8.3.163
232:Sequence alignment
81:originally coined
63:Bayesian inference
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1120:Maximum parsimony
1113:Inference methods
1061:Phylogenetic tree
442:(6642): 539–547.
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618:Genome Biology
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577:Bioinformatics
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1325:Sister group
1308:Nomenclature
1271:Autapomorphy
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1234:Group traits
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1320:Crown group
1282:Group types
1013:Systematics
928:: 541–562.
182:haptophytes
158:convergence
1382:Categories
998:Cladistics
624:(4): R36.
524:(6): e77.
243:References
178:rhizarians
174:alveolates
1335:Supertree
1299:Polyphyly
1294:Paraphyly
1289:Monophyly
1261:Apomorphy
1241:Primitive
1184:PhyloCode
1066:Cladogram
673:CiteSeerX
348:206580993
316:Pennisi E
237:Supertree
202:PhylomeDB
196:Databases
102:H. pylori
97:H. pylori
24:evolution
1388:Genomics
1354:Category
1257:Derived
1003:Taxonomy
907:23617542
856:22628470
807:18522922
758:16490279
703:16379422
695:15861208
650:19368726
599:14734307
558:16846248
340:18583591
302:21873298
208:See also
116:taxonomy
28:genomics
1366:Commons
1092:Lineage
898:3637829
847:3396900
798:2610160
641:2688927
549:1484587
526:Bibcode
499:9521918
458:9252185
417:9334711
408:3155951
320:Science
293:3258035
166:species
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170:plants
32:genome
1330:Basal
1155:UPGMA
1087:Grade
1083:Clade
734:(PDF)
699:S2CID
344:S2CID
77:When
903:PMID
852:PMID
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754:PMID
691:PMID
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595:PMID
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454:PMID
413:PMID
336:PMID
298:PMID
184:and
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65:or
26:and
1085:vs
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